Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate GFF2918 PGA1_c29650 succinate-semialdehyde dehdyrogenase GabD
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Phaeo:GFF2918 Length = 491 Score = 320 bits (821), Expect = 5e-92 Identities = 184/475 (38%), Positives = 270/475 (56%), Gaps = 8/475 (1%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73 +I G FV DG TF NPA + + VA+ +++ A+ A+ A W K T ER Sbjct: 23 YIGGAFVDGADG-TFAVKNPARGDVIANVADVSRSQVAGAIAQAEVAQKD-WAKWTGKER 80 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 VLRK DL++E +E+L+V+ + + GKP S +I A FF++ + I E Sbjct: 81 ANVLRKWFDLMMENQEDLAVILTAEMGKPLAESRG-EIGYGASFIEFFAEEAKRIYGETI 139 Query: 134 --QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTAT 191 D + +++P+GV I PWN P ++T K PALAAG V +PAELTP++AT Sbjct: 140 PGHQRDKRIT-VLKQPIGVAASITPWNFPNAMITRKAGPALAAGCAFVARPAELTPLSAT 198 Query: 192 VLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTL 251 LA + AG+P GV N+V + G E+ V ++FTG T G+I+M AA T+ Sbjct: 199 ALAVLADRAGIPAGVFNVVTSSNASETGKEFCENNAVRKLTFTGSTEVGRILMRQAADTV 258 Query: 252 KRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKF 311 + S ELGG P ++F D++LD +E + F N G+ C+C +RIYV+ Y+AF K Sbjct: 259 MKCSMELGGNAPFIVFDDADLDAAVEGAIMCKFRNNGQTCVCANRIYVQAGVYDAFAAKL 318 Query: 312 VAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYF 371 ++ VGD T+ G LI+++ E+V +I A E+G ++ GG E G F Sbjct: 319 KEAVAKMTVGDGLAEGTQFGPLINEKAVEKVQAHIADAKEKGAEVILGGNPSE--LGGTF 376 Query: 372 LEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAH 431 EPTIITG T+D ++E FGP+ + F+TE++V+E NDT +GL++ + DL R + Sbjct: 377 FEPTIITGATQDMVFSQDETFGPMAPLFKFETEDDVIEMANDTIFGLASYFYAKDLSRVY 436 Query: 432 RVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 +VA +E GIV VNT + PFGG+KQSG+GREG H E Y E+ IC+ + Sbjct: 437 KVAEALEYGIVGVNTGIISTELAPFGGVKQSGLGREGSHHGIEDYLEMKYICMSV 491 Lambda K H 0.318 0.136 0.404 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 571 Number of extensions: 23 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 486 Length of database: 491 Length adjustment: 34 Effective length of query: 452 Effective length of database: 457 Effective search space: 206564 Effective search space used: 206564 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory